Starting phenix.real_space_refine (version: dev) on Mon Feb 20 22:39:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoy_33363/02_2023/7xoy_33363_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoy_33363/02_2023/7xoy_33363.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoy_33363/02_2023/7xoy_33363_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoy_33363/02_2023/7xoy_33363_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoy_33363/02_2023/7xoy_33363_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoy_33363/02_2023/7xoy_33363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoy_33363/02_2023/7xoy_33363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoy_33363/02_2023/7xoy_33363_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoy_33363/02_2023/7xoy_33363_trim_updated.pdb" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "C ASP 96": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13264 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3294 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 29, 'TRANS': 428} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3294 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 29, 'TRANS': 428} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3294 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 29, 'TRANS': 428} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "D" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3294 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 29, 'TRANS': 428} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'peptide': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'peptide': 1} Time building chain proxies: 7.93, per 1000 atoms: 0.60 Number of scatterers: 13264 At special positions: 0 Unit cell: (104.13, 143.91, 81.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 4 15.00 O 2536 8.00 N 2336 7.00 C 8336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.08 Conformation dependent library (CDL) restraints added in 2.2 seconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 20 sheets defined 38.0% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'B' and resid 7 through 10 Processing helix chain 'B' and resid 43 through 58 removed outlier: 3.516A pdb=" N LYS B 50 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 128 through 138 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 151 through 160 removed outlier: 3.618A pdb=" N HIS B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 169 Processing helix chain 'B' and resid 184 through 197 removed outlier: 3.913A pdb=" N GLU B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 214 No H-bonds generated for 'chain 'B' and resid 212 through 214' Processing helix chain 'B' and resid 249 through 262 removed outlier: 4.000A pdb=" N ASP B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET B 254 " --> pdb=" O ASP B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 283 removed outlier: 3.979A pdb=" N GLU B 282 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 303 removed outlier: 3.705A pdb=" N SER B 303 " --> pdb=" O GLY B 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 300 through 303' Processing helix chain 'B' and resid 310 through 313 No H-bonds generated for 'chain 'B' and resid 310 through 313' Processing helix chain 'B' and resid 330 through 335 Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 389 through 395 Processing helix chain 'B' and resid 406 through 408 No H-bonds generated for 'chain 'B' and resid 406 through 408' Processing helix chain 'B' and resid 423 through 432 removed outlier: 4.633A pdb=" N ASP B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 459 Processing helix chain 'A' and resid 7 through 10 Processing helix chain 'A' and resid 43 through 58 removed outlier: 3.540A pdb=" N ARG A 46 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 100 through 108 Processing helix chain 'A' and resid 128 through 138 Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 151 through 160 removed outlier: 3.606A pdb=" N HIS A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 169 Processing helix chain 'A' and resid 184 through 197 removed outlier: 3.914A pdb=" N GLU A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 249 through 262 removed outlier: 3.999A pdb=" N ASP A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 283 removed outlier: 4.179A pdb=" N GLU A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 303 removed outlier: 3.706A pdb=" N SER A 303 " --> pdb=" O GLY A 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 300 through 303' Processing helix chain 'A' and resid 310 through 313 No H-bonds generated for 'chain 'A' and resid 310 through 313' Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 423 through 432 removed outlier: 4.633A pdb=" N ASP A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'C' and resid 7 through 10 Processing helix chain 'C' and resid 43 through 58 removed outlier: 3.575A pdb=" N ARG C 46 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 86 removed outlier: 3.592A pdb=" N ALA C 80 " --> pdb=" O GLY C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 108 Processing helix chain 'C' and resid 128 through 138 Processing helix chain 'C' and resid 147 through 149 No H-bonds generated for 'chain 'C' and resid 147 through 149' Processing helix chain 'C' and resid 151 through 160 removed outlier: 3.602A pdb=" N HIS C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 169 Processing helix chain 'C' and resid 184 through 197 removed outlier: 4.880A pdb=" N ALA C 189 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS C 194 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C 196 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 214 No H-bonds generated for 'chain 'C' and resid 212 through 214' Processing helix chain 'C' and resid 249 through 262 removed outlier: 4.017A pdb=" N ASP C 253 " --> pdb=" O SER C 249 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET C 254 " --> pdb=" O ASP C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 283 removed outlier: 4.187A pdb=" N GLU C 282 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU C 283 " --> pdb=" O LYS C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 303 removed outlier: 3.670A pdb=" N SER C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 300 through 303' Processing helix chain 'C' and resid 310 through 313 No H-bonds generated for 'chain 'C' and resid 310 through 313' Processing helix chain 'C' and resid 330 through 335 Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 389 through 395 Processing helix chain 'C' and resid 406 through 408 No H-bonds generated for 'chain 'C' and resid 406 through 408' Processing helix chain 'C' and resid 423 through 432 removed outlier: 4.645A pdb=" N ASP C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 459 Processing helix chain 'D' and resid 7 through 10 Processing helix chain 'D' and resid 43 through 58 removed outlier: 3.569A pdb=" N ARG D 46 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 86 Processing helix chain 'D' and resid 100 through 108 Processing helix chain 'D' and resid 128 through 138 Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'D' and resid 151 through 160 removed outlier: 3.621A pdb=" N HIS D 157 " --> pdb=" O GLY D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 169 Processing helix chain 'D' and resid 184 through 197 removed outlier: 4.636A pdb=" N ALA D 189 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS D 194 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL D 196 " --> pdb=" O LEU D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 214 No H-bonds generated for 'chain 'D' and resid 212 through 214' Processing helix chain 'D' and resid 249 through 262 removed outlier: 4.017A pdb=" N ASP D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET D 254 " --> pdb=" O ASP D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 283 removed outlier: 4.185A pdb=" N GLU D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 303 removed outlier: 3.667A pdb=" N SER D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 300 through 303' Processing helix chain 'D' and resid 310 through 313 No H-bonds generated for 'chain 'D' and resid 310 through 313' Processing helix chain 'D' and resid 330 through 335 Processing helix chain 'D' and resid 353 through 363 Processing helix chain 'D' and resid 389 through 395 Processing helix chain 'D' and resid 406 through 408 No H-bonds generated for 'chain 'D' and resid 406 through 408' Processing helix chain 'D' and resid 423 through 432 removed outlier: 4.642A pdb=" N ASP D 432 " --> pdb=" O LYS D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 459 Processing sheet with id= A, first strand: chain 'B' and resid 16 through 18 removed outlier: 5.848A pdb=" N ILE B 290 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LYS B 33 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B 292 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 66 through 69 removed outlier: 6.400A pdb=" N LYS B 89 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N GLU B 69 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 91 " --> pdb=" O GLU B 69 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 204 through 208 removed outlier: 7.194A pdb=" N GLU B 242 " --> pdb=" O GLY B 205 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ASP B 207 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE B 244 " --> pdb=" O ASP B 207 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 367 through 370 Processing sheet with id= E, first strand: chain 'B' and resid 435 through 439 Processing sheet with id= F, first strand: chain 'A' and resid 16 through 18 removed outlier: 5.896A pdb=" N ILE A 290 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LYS A 33 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A 292 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 66 through 69 removed outlier: 6.402A pdb=" N LYS A 89 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N GLU A 69 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A 91 " --> pdb=" O GLU A 69 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 204 through 208 removed outlier: 7.195A pdb=" N GLU A 242 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ASP A 207 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE A 244 " --> pdb=" O ASP A 207 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'A' and resid 367 through 370 Processing sheet with id= J, first strand: chain 'A' and resid 435 through 439 Processing sheet with id= K, first strand: chain 'C' and resid 16 through 18 removed outlier: 5.872A pdb=" N ILE C 290 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LYS C 33 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL C 292 " --> pdb=" O LYS C 33 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 66 through 69 removed outlier: 6.407A pdb=" N LYS C 89 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N GLU C 69 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL C 91 " --> pdb=" O GLU C 69 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 204 through 208 removed outlier: 7.196A pdb=" N GLU C 242 " --> pdb=" O GLY C 205 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ASP C 207 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE C 244 " --> pdb=" O ASP C 207 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'C' and resid 367 through 370 Processing sheet with id= O, first strand: chain 'C' and resid 435 through 439 Processing sheet with id= P, first strand: chain 'D' and resid 16 through 18 removed outlier: 5.871A pdb=" N ILE D 290 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LYS D 33 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL D 292 " --> pdb=" O LYS D 33 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 66 through 69 removed outlier: 6.404A pdb=" N LYS D 89 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N GLU D 69 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL D 91 " --> pdb=" O GLU D 69 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'D' and resid 204 through 208 removed outlier: 7.193A pdb=" N GLU D 242 " --> pdb=" O GLY D 205 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N ASP D 207 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE D 244 " --> pdb=" O ASP D 207 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'D' and resid 367 through 370 Processing sheet with id= T, first strand: chain 'D' and resid 435 through 439 402 hydrogen bonds defined for protein. 990 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.79 Time building geometry restraints manager: 6.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2830 1.33 - 1.45: 2924 1.45 - 1.57: 7690 1.57 - 1.69: 4 1.69 - 1.81: 88 Bond restraints: 13536 Sorted by residual: bond pdb=" C PRO A 70 " pdb=" O PRO A 70 " ideal model delta sigma weight residual 1.235 1.205 0.030 7.90e-03 1.60e+04 1.41e+01 bond pdb=" N ILE B 180 " pdb=" CA ILE B 180 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.79e+00 bond pdb=" N VAL B 98 " pdb=" CA VAL B 98 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.57e+00 bond pdb=" N ILE A 180 " pdb=" CA ILE A 180 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.25e-02 6.40e+03 8.47e+00 bond pdb=" N VAL D 98 " pdb=" CA VAL D 98 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.39e+00 ... (remaining 13531 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.64: 567 106.64 - 113.48: 7431 113.48 - 120.32: 5052 120.32 - 127.17: 5235 127.17 - 134.01: 155 Bond angle restraints: 18440 Sorted by residual: angle pdb=" C GLY C 76 " pdb=" N VAL C 77 " pdb=" CA VAL C 77 " ideal model delta sigma weight residual 120.88 113.82 7.06 1.22e+00 6.72e-01 3.35e+01 angle pdb=" N THR C 75 " pdb=" CA THR C 75 " pdb=" C THR C 75 " ideal model delta sigma weight residual 111.07 105.64 5.43 1.07e+00 8.73e-01 2.58e+01 angle pdb=" N THR A 182 " pdb=" CA THR A 182 " pdb=" C THR A 182 " ideal model delta sigma weight residual 113.18 107.49 5.69 1.21e+00 6.83e-01 2.21e+01 angle pdb=" N THR C 182 " pdb=" CA THR C 182 " pdb=" C THR C 182 " ideal model delta sigma weight residual 113.19 107.76 5.43 1.19e+00 7.06e-01 2.08e+01 angle pdb=" C ALA C 343 " pdb=" CA ALA C 343 " pdb=" CB ALA C 343 " ideal model delta sigma weight residual 116.54 111.46 5.08 1.15e+00 7.56e-01 1.95e+01 ... (remaining 18435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 7460 16.68 - 33.37: 366 33.37 - 50.05: 137 50.05 - 66.74: 50 66.74 - 83.42: 7 Dihedral angle restraints: 8020 sinusoidal: 2916 harmonic: 5104 Sorted by residual: dihedral pdb=" CA LYS C 97 " pdb=" C LYS C 97 " pdb=" N VAL C 98 " pdb=" CA VAL C 98 " ideal model delta harmonic sigma weight residual 180.00 160.84 19.16 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ARG D 335 " pdb=" CB ARG D 335 " pdb=" CG ARG D 335 " pdb=" CD ARG D 335 " ideal model delta sinusoidal sigma weight residual 60.00 119.92 -59.92 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG A 335 " pdb=" CB ARG A 335 " pdb=" CG ARG A 335 " pdb=" CD ARG A 335 " ideal model delta sinusoidal sigma weight residual 60.00 119.71 -59.71 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 8017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1478 0.052 - 0.103: 481 0.103 - 0.155: 82 0.155 - 0.206: 20 0.206 - 0.258: 7 Chirality restraints: 2068 Sorted by residual: chirality pdb=" CA VAL A 93 " pdb=" N VAL A 93 " pdb=" C VAL A 93 " pdb=" CB VAL A 93 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA VAL A 114 " pdb=" N VAL A 114 " pdb=" C VAL A 114 " pdb=" CB VAL A 114 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA VAL B 114 " pdb=" N VAL B 114 " pdb=" C VAL B 114 " pdb=" CB VAL B 114 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 2065 not shown) Planarity restraints: 2440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 277 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C ALA D 277 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA D 277 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU D 278 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 277 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C ALA C 277 " -0.038 2.00e-02 2.50e+03 pdb=" O ALA C 277 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU C 278 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 277 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C ALA A 277 " -0.037 2.00e-02 2.50e+03 pdb=" O ALA A 277 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 278 " 0.013 2.00e-02 2.50e+03 ... (remaining 2437 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 3575 2.78 - 3.31: 14484 3.31 - 3.84: 21803 3.84 - 4.37: 25295 4.37 - 4.90: 39690 Nonbonded interactions: 104847 Sorted by model distance: nonbonded pdb=" N GLN C 147 " pdb=" OE1 GLN C 147 " model vdw 2.255 2.520 nonbonded pdb=" N GLN D 147 " pdb=" OE1 GLN D 147 " model vdw 2.261 2.520 nonbonded pdb=" N LYS B 401 " pdb=" OD2 ASP B 404 " model vdw 2.274 2.520 nonbonded pdb=" N LYS A 401 " pdb=" OD2 ASP A 404 " model vdw 2.277 2.520 nonbonded pdb=" OD1 ASP D 250 " pdb=" NH1 ARG D 318 " model vdw 2.278 2.520 ... (remaining 104842 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 52 5.16 5 C 8336 2.51 5 N 2336 2.21 5 O 2536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.240 Check model and map are aligned: 0.220 Process input model: 36.930 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.140 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.037 13536 Z= 0.434 Angle : 0.732 7.064 18440 Z= 0.467 Chirality : 0.053 0.258 2068 Planarity : 0.004 0.041 2440 Dihedral : 12.508 83.421 4804 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 45.15 Ramachandran Plot: Outliers : 1.15 % Allowed : 10.20 % Favored : 88.65 % Rotamer Outliers : 8.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.20), residues: 1824 helix: -0.75 (0.20), residues: 700 sheet: -2.22 (0.39), residues: 176 loop : -2.52 (0.20), residues: 948 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 310 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 24 residues processed: 380 average time/residue: 0.2942 time to fit residues: 153.7693 Evaluate side-chains 217 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 193 time to evaluate : 1.549 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1307 time to fit residues: 7.6930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 4.9990 chunk 136 optimal weight: 0.0770 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 105 optimal weight: 0.5980 chunk 163 optimal weight: 3.9990 overall best weight: 1.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 13536 Z= 0.255 Angle : 0.690 8.554 18440 Z= 0.348 Chirality : 0.047 0.219 2068 Planarity : 0.006 0.044 2440 Dihedral : 5.567 78.017 2008 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.94 % Favored : 90.90 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.20), residues: 1824 helix: -0.81 (0.19), residues: 720 sheet: -2.52 (0.34), residues: 204 loop : -2.04 (0.22), residues: 900 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 245 average time/residue: 0.2463 time to fit residues: 87.6195 Evaluate side-chains 158 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 1.646 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1144 time to fit residues: 2.3224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 136 optimal weight: 0.0770 chunk 111 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 176 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 13536 Z= 0.247 Angle : 0.646 8.201 18440 Z= 0.326 Chirality : 0.045 0.181 2068 Planarity : 0.005 0.045 2440 Dihedral : 5.669 86.019 2008 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.22 % Favored : 91.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.20), residues: 1824 helix: -0.85 (0.18), residues: 748 sheet: -1.87 (0.34), residues: 216 loop : -1.93 (0.23), residues: 860 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2331 time to fit residues: 79.5611 Evaluate side-chains 159 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.551 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 173 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 13536 Z= 0.353 Angle : 0.700 7.463 18440 Z= 0.356 Chirality : 0.047 0.200 2068 Planarity : 0.006 0.043 2440 Dihedral : 6.312 88.741 2008 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.65 % Favored : 90.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.20), residues: 1824 helix: -0.95 (0.18), residues: 752 sheet: -1.90 (0.32), residues: 264 loop : -1.73 (0.23), residues: 808 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2350 time to fit residues: 67.9755 Evaluate side-chains 145 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.472 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 129 optimal weight: 0.0770 chunk 71 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 367 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 367 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 13536 Z= 0.182 Angle : 0.602 8.433 18440 Z= 0.305 Chirality : 0.044 0.142 2068 Planarity : 0.005 0.043 2440 Dihedral : 6.001 84.920 2008 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.51 % Favored : 92.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.20), residues: 1824 helix: -0.60 (0.18), residues: 752 sheet: -1.72 (0.35), residues: 232 loop : -1.50 (0.23), residues: 840 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2367 time to fit residues: 72.9513 Evaluate side-chains 164 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.499 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 174 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 5 GLN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 HIS ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 13536 Z= 0.231 Angle : 0.619 7.692 18440 Z= 0.313 Chirality : 0.045 0.150 2068 Planarity : 0.005 0.043 2440 Dihedral : 5.910 88.304 2008 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.66 % Favored : 91.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.20), residues: 1824 helix: -0.52 (0.19), residues: 756 sheet: -0.86 (0.41), residues: 184 loop : -1.54 (0.23), residues: 884 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2327 time to fit residues: 68.3534 Evaluate side-chains 160 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.559 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 127 optimal weight: 0.0870 chunk 98 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 173 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 13536 Z= 0.213 Angle : 0.612 7.809 18440 Z= 0.309 Chirality : 0.044 0.146 2068 Planarity : 0.005 0.059 2440 Dihedral : 5.854 78.880 2008 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.06 % Favored : 91.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.21), residues: 1824 helix: -0.44 (0.19), residues: 760 sheet: -0.55 (0.43), residues: 184 loop : -1.46 (0.23), residues: 880 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2342 time to fit residues: 68.1218 Evaluate side-chains 153 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.545 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 33 optimal weight: 0.3980 chunk 110 optimal weight: 0.1980 chunk 118 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 13536 Z= 0.202 Angle : 0.616 10.043 18440 Z= 0.309 Chirality : 0.044 0.148 2068 Planarity : 0.005 0.049 2440 Dihedral : 5.743 83.408 2008 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.55 % Favored : 91.39 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.21), residues: 1824 helix: -0.32 (0.19), residues: 760 sheet: -0.37 (0.38), residues: 224 loop : -1.48 (0.23), residues: 840 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2214 time to fit residues: 65.4112 Evaluate side-chains 152 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.577 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 13536 Z= 0.352 Angle : 0.701 13.672 18440 Z= 0.352 Chirality : 0.047 0.158 2068 Planarity : 0.005 0.043 2440 Dihedral : 6.041 82.428 2008 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.38 % Favored : 90.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.20), residues: 1824 helix: -0.42 (0.19), residues: 756 sheet: -0.32 (0.39), residues: 224 loop : -1.55 (0.23), residues: 844 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2241 time to fit residues: 61.3467 Evaluate side-chains 139 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.587 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 13536 Z= 0.203 Angle : 0.626 6.963 18440 Z= 0.314 Chirality : 0.044 0.154 2068 Planarity : 0.005 0.042 2440 Dihedral : 5.965 86.331 2008 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.89 % Favored : 92.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.21), residues: 1824 helix: -0.18 (0.19), residues: 744 sheet: -0.17 (0.38), residues: 232 loop : -1.41 (0.23), residues: 848 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2307 time to fit residues: 64.0176 Evaluate side-chains 139 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.663 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 59 optimal weight: 0.0170 chunk 146 optimal weight: 0.0570 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.101222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.082763 restraints weight = 29285.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.085478 restraints weight = 17144.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.087389 restraints weight = 11684.691| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 13536 Z= 0.212 Angle : 0.636 8.521 18440 Z= 0.317 Chirality : 0.044 0.149 2068 Planarity : 0.005 0.041 2440 Dihedral : 5.885 82.401 2008 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.33 % Favored : 91.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.21), residues: 1824 helix: -0.14 (0.19), residues: 744 sheet: -0.09 (0.38), residues: 232 loop : -1.35 (0.23), residues: 848 =============================================================================== Job complete usr+sys time: 2393.38 seconds wall clock time: 44 minutes 10.56 seconds (2650.56 seconds total)